Supervisors and Projects
The supervisors below are offering DPhil projects for 2024 entry. It may be possible to convert some of these projects into MSc and other projects may also be available. Please contact supervisors directly to enquire.
The lab is interested in the neurobiology of emergent higher order cognition across all levels of analysis. To date we have largely explored the contribution of locally projecting GABAergic interneurons to early sensory perception in somatosensory (Anastasiades et al., 2016; Baruchin et al., 2022; Ghezzi et al., 2021; Marques-Smith et al., 2016) and visual cortex (Ghezzi et al., in preparation). These studies have identified differences in the construction of formative circuits that mirror the requirements for early function. The lab is now interested in understanding how circuits are co-ordinated at the brain wide level from the molecular to systems level. To this end we are interested in attracting DPhil students who are keen to pursue individually tailored projects using advanced techniques from patch-seq to multi-photon imaging of neurotransmitter dynamics. We collaborate closely with other groups in the department, notably those of Prof. Armin Lak (prefrontal cortex function and behaviour) and Adam Packer (claustrum and advanced optical approaches). Students are welcome to contact Prof. Simon Butt to discuss further but are encouraged to read recent publications from the group and bring their own ideas.
We are at an exciting turning point in neuroscience. New technologies now allow us to measure and control neural activity and behaviour with unprecedented detail (Landhuis et al. Nature 2017, Lauer et al. Nature Methods 2022). At the same time, new theoretical frameworks are starting to reveal how rich behaviours arise from synaptic, circuit and systems computations (Richards et al. Nature Neuroscience 2019). We are contributing directly to the latter by aiming to understand how we learn. To this end, we are developing a new generation of computational models of brain function guided by deep learning principles. We focus on understanding how a given behavioural outcome ultimately leads to credit being assigned to trillions of synapses across multiple brain areas – the credit assignment problem. To survive and adapt to dynamic and complex environments animals and humans must assign credit efficiently. Recently, we have shown that the brain can approximate deep learning algorithms (Sacramento et al. NeurIPS 2018, Blake et al. Nature Neuroscience 2019, Greedy et al. NeurIPS 2022, Boven et al. Nature Comms 2023). In this project, you will build on state-of-the-art computational models of AI-like credit assignment in the brain and contrast it with recent experimental observations at the behavioural, systems and circuit level.
The neurotransmitter dopamine in the striatum is critical to our motivated actions, and is dysregulated in disorders spanning from Parkinson’s disease (PD) to addictions. Midbrain dopamine neurons form intriguing structures: they give rise to colossal axonal arbours that are more branched than any other neuron type, providing opportunities for diverse neuromodulators to act on axons to shape dopamine function. We have discovered striatal circuits that can act on dopamine axons to powerfully transform dopamine output. We are working to better understand the diverse range of striatal neuromodulators and circuits, neuronal and non-neuronal, that act on dopamine axons to govern dopamine output, in mouse brain ex vivo in health and their disturbances in mouse models of PD. Potential DPhil projects will join our effort to reveal the striatal modulators and circuits that govern dopamine transmission, and to understand the dynamic signalling profiles of those neuromodulators and circuits. Research techniques involved will include state-of-the-art methods for the direct detection of neurotransmitters and neuromodulators in real-time, such as imaging genetically encoded fluorescent reporters for neuromodulators (e.g. GRAB sensors to detect amines, neuropeptides, lipid transmitters) or cellular activity (calcium and voltage sensors), alongside fast-scan cyclic voltammetry for real-time detection of dopamine and/or neuronal recordings with electrophysiology, in conjunction with methods to manipulate brain and cells (optogenetics, chemogenetics, pharmacology) in ex vivo brain slices from healthy mice and transgenic models of PD.
Sex differences often represent the most dramatic intraspecific variations seen in nature. Although males and females share the same genome and have similar nervous systems, they differ profoundly in reproductive investments and require distinct morphological, physiological, and behavioural adaptations. Animals determine sex early in development, which initiates many irreversible differentiation events that influence how the genome and environment interact to produce sexspecific behaviours. Across taxa, these events converge to regulate sexually dimorphic gene expression, which specifies sex-typical development and neural circuit function. However, the molecular programs that act during development remain largely unknown. We aim to understand the gene regulatory networks underlying sexually dimorphic neuronal development in the brain of the genetically tractable vinegar fly Drosophila melanogaster. Given the long and fruitful history of using vinegar flies to uncover fundamental principles of developmental biology and behavioural neuroscience, they are ideally suited for studies which bridge these disciplines. The fly's central brain is a remarkably complex tissue composed of approximately 100,000 interconnected neurons, forming the intricate networks necessary to coordinate complex cognitive and motor functions. Tightly regulated molecular programs act over a broad developmental window leading to the diversity of cell types found in the brain. New advances in single-cell technologies have enabled, for the first time, a comprehensive survey of this diversity throughout development. As sex plays distinct roles in different neurons at different developmental times, we only now have the means of studying the emergence of sexual dimorphisms within this complex structure. We will use single-cell technologies to compare the molecular profiles of both males and females in the developing central brain to understand the mechanisms underlying sexual dimorphism in the nervous system. This timely study will also generate the first developmental single-cell gene expression atlas of the Drosophila central brain, an immensely beneficial resource that will be available and accessible to the research community. More broadly, our findings will generate a unique resource to investigate general mechanisms underlying the development and functions of neuronal circuits for the fly community and beyond, given that many of the fundamental biochemical pathways and mechanisms are conserved between flies and humans. The proposed experiments will paint a detailed picture of cellular and molecular diversity in a developing central nervous system. Our data will answer the longstanding question: How are neuron types associated with sexual behaviours born and wired?
Animals must navigate complex visual environments, ensuring they avoid dangers while also foraging for food or finding a mate. To succeed, animals must identify relevant visual cues and interpret them in relation to their external circumstances and internal state, ensuring they respond appropriately. Visual information is perceived non-discriminately in the eye; however, how the animal responds to this information is determined in the brain. Understanding how the brain transforms complex visual stimuli into complex behaviour patterns remains a significant challenge in behavioural neuroscience. The elegant courtship display of the male vinegar fly Drosophila melanogaster is ideally suited to address this challenge. To reproduce successfully, Drosophila males are hardwired, having the ability to navigate complex environments and identify a mate. The interpretation of the female as a potential mate triggers a behavioural switch in males, setting off an elaborate behavioural display: males persistently pursue the female while intermittently singing her a courtship song through the extension and vibration of a single wing. Meanwhile, the female continuously decamps and rejects the male's advances, giving her time to assess his suitability as a mate before she sanctions the mating. This switch in the males' behavioural pattern is triggered when a sexual arousal threshold is reached, a stable internal state ensuring males persist in pursuing the female. Interestingly, this behavioural switch must also be flexible. If males, once aroused, find the female is, in fact, a different species or sex, they must switch back to their pre-arousal behavioural patterns. Studies in the vinegar fly Drosophila melanogaster can provide insights into general principles of how brains use sensory information, like visual stimuli, to guide behaviour and how internal state changes, such as arousal, modify these sensorimotor programs. Working with flies has the advantage of using a vast array of genetic tools that allows us to identify and manipulate relevant neurons in the brain. Using these tools, we will study a group of sexually-dimorphic neurons involved in visual integration critical to male courtship behaviour and reproductive success.This proposal will be an ideal entry point into our understanding of how animals integrate external sensory information with their internal state to make an appropriate context-dependent decision.
Diabetes affects around 1/10 people in the UK, with the majority having type 2 diabetes. Despite causing complications in many organs in the body, the leading cause of mortality in people with type 2 diabetes is cardiovascular disease. Diabetes is a metabolic disease, changing substrates supplied to and those utilised by the heart. However, it is currently unclear why abnormal cardiac metabolism deleteriously affects the heart, causing diabetic cardiomyopathy (DCM) and heart failure with preserved ejection fraction (HFpEF). These are important questions to answer as we currently have no treatments for DCM or HFpEF. In our lab we are trying to understand what processes metabolism regulates within the cell. Specifically, we are studying the role of metabolites as regulators of cell function, due to their ability to regulate transcription factors, post-translational modifications, and as allosteric regulators of enzyme function. Thus, metabolites are not simply sources of energy, but also regulated signalling molecules that can determine rates of transcription, trafficking and enzyme activity. We have shown previously that metabolites can regulate signalling processes in many compartments in the cell, including the mitochondria, nucleus, cell membrane and cytosol. We have shown that in diabetes when the concentration of these metabolites changes within the heart, this has consequences for many cellular processes such as the response to ischaemia, increased workload and change in nutrition. We use a range of techniques including cell culture, heart perfusion, in vivo imaging, metabolomics, and molecular biology approaches. We are interested in understanding whether pharmacologically targeting metabolism is beneficial for the diabetic heart.
Neurons in auditory cortex produce patterns of spikes in response to sound. What is the computational mapping from sound to auditory cortical responses? Can we predict the moment-to-moment responses of neurons in the auditory cortex to arbitrary sounds? This computational project involves fitting various models to the mapping from natural sounds to neural responses recorded from the midbrain and auditory cortex. The project will begin with a fitting a simple model, the linear-nonlinear model, and testing its capacity to predict neural responses to a held-out dataset of sounds. The student will then go on to analyse the linear and nonlinear parts of this model to look for different types of neuron and extend this work to include more complex network models that better reflect the physiological properties of auditory neurons and the way information processing changes between the midbrain and cortex. The structure of these more complex networks will be analysed to provide insight into the functional organization of the auditory brain.
How fat tissue secretes fatty acids during times of starvation is a big unanswered question in cell physiology. In fact, we know in general relatively little about the mechanisms that traffic free fatty acids into and out of cells. In your project, we tackle this problem with a tissue culture model for adipocytes, using a combination of light and electron microscopy, structural biology, easy metabolite analysis, cell biology and CRISPR-genetics. The experimental set up is easily tractable because the secretion of fatty acids can be readily induced by addition of a small molecule to differentiated adipocytes. You will focus on studying the intracellular re-arrangement of organelles during lipolysis. We will investigate how the lipid storage organelles called lipid droplets are hooked to the cell surface and how this is coupled to efficient secretion of newly mobilized fatty acids. This will be analyzed by light and electron-microscopy, and metabolic essays. To identify factors that move the lipid droplets around in the cell we are going to use organelle purification and proximity specific proteomics methods. A candidate library of potentially important factors will then be subjected to a targeted genetic screen in which we aim to find the machinery that transports fatty acids outside of the cell. These mechanisms have fundamental relevance in systemic energy metabolism and will help to understand the pathophysiology of obesity and diabetes.
Mitochondria are best known for their role in energy metabolism but have recently emerged as critical signalling hubs which are important during cellular differentiation from stem cells. Metabolic adaptability is crucial in decision making processes called “fate switches”. The machinery which controls these processes is beginning to emerge but many central questions remain unanswered. We have recently discovered that mitochondrial contact sites with other organelles in the cell are critical in regulating these processes. The contact site factors establish physical interactions with e.g. the endoplasmic reticulum and specialize in importing specific lipids that remodel the shape, function and biochemical activity of mitochondria. These changes in turn determine the fate of the cell and control mechanism that establish new cellular identity. This PhD project will use CRISPR-genetics in combination with fluorescence microscopy and easy to study metabolic readouts to discover the cell biological mechanisms by which mitochondria remodel their function. We focus on a mitochondrial contact site protein, which, according to its phosphorylation status can interact with different organelles in the cell. The selection of preferred binding partners within the mitochondrial neighbourhood has profound consequences on mitochondrial function and cell fate. We have evidence from mass spectrometry experiments that mitochondrial import of specific lipids modulates the mitochondrial function depending on which other organelle is bound. How cell biological mechanisms organize organelle neighbourhoods and inter-organelle communication is an exciting new area in the molecular life sciences and has relevance in all cell-types which are metabolically active such as fat cells, liver, neurons and muscles.
How the brain integrates external sensory signals with internal reward and motivational signals for making decisions? How the brain learns over time to make better decisions? Our aim is to find quantitative circuit-level answers to these questions. We particularly focus on understanding the roles that frontal-striatal circuits play during decision-making, and how neuromodulators, in particular the dopamine signals, shape these circuits to guide learning. We employ a multi-disciplinary approach including high-count electrophysiology, multi-photon imaging, optogenetics, highly-controlled behavioural tasks in mice, and extensive computational modelling. Projects in the lab can be flexible along these themes, and may include experiments as well as computational work.
Historically, understanding of iron’s importance for physiology and medicine has been centred around haemoglobin, and iron deficiency has been synonymous with anaemia. However, the past decade has seen a paradigm shift in our understanding of the physiological importance of iron, and we now know that non-haemoglobin iron is essential for fundamental processes within the cardiovascular system, such as contractile function of the heart and regulation of vascular tone. In clinical practice, the growing recognition of the importance of iron has led to greater focus on the treatment of non-anaemic iron deficiency, particularly in heart failure. However, this change in clinical practice remains uncoupled from mechanistic understanding of where and how iron exerts its effects. To address this problem, our research combines clinical studies of functional and iron parameters in heart failure patients with mechanistic studies in preclinical models of heart failure. Techniques range from proteomic and metabolomic characterisation of patient samples, to advanced MR imaging of Heart function in pre-clinical models, to cell-based work in cardiac and vascular cells. The aim is to understand how non-anaemic iron deficiency affects heart failure patients, and use that understanding to implement optimal iron replacement therapies.
Cardiovascular diseases are a leading cause of death worldwide. They result from a variety of factors, including genetics, lifestyle, and environmental exposures. This project aims to investigate the use of human induced pluripotent stem cell (hiPSC) derived cardiomyocytes and cardiac organoids as disease models to explore novel therapeutic avenues for cardiovascular diseases such as cardiac arrhythmia, hypertrophy, and diabetic cardiomyopathy. The core of this project involves developing hiPSC-derived cardiomyocytes and cardiac organoids that faithfully recapitulate disease pathology. Furthermore, our proposal extends to the realm of neurocardiac interactions by introducing hiPSC-derived sympathetic neurons into the model. By establishing neuronal-cardiac co-culture systems, we will gain insights into how the nervous system influences cardiac function in health and disease. Cutting-edge techniques, such as Fluorescence Resonance Energy Transfer (FRET) and calcium imaging will be employed for precise measurement of intracellular signaling dynamics. Additionally, we will use state-of-the-art methodologies, including optical mapping and electrical mapping using a Microelectrode Array (MEA) system, to comprehensively analyze the electrophysiological properties of the models. The results of this project will provide new insights into the mechanisms of cardiac diseases and could ultimately lead to new treatments and prevention strategies.
Stress exacerbates many psychiatric conditions, and repeated stress contributes to the pathogenesis of disorders such as Post Traumatic Stress Disorder, Panic Disorder and Major Depressive Disorder. The orexin (hypocretin) system is highly reactive to stress, and regulates many physiological processes that are altered in stress-related mental illness, including sleep/wake patterns, appetite and cognition. Changes in orexin levels have been reported in major depression and anxiety disorders, and polymorphisms in the orexin 1 receptor are associated with anxiety spectrum disorders, particularly in women. The orexin system is therefore an attractive target for treating stress-related disorders. Orexinergic neurons have wide projection targets across the nervous system, including hypothalamus, thalamus, cortex, brain stem and spinal cord. The projections to other hypothalamic neurons and subcortical arousal centres are important for modulating arousal, appetite and activity of the Hypothalamic Pituitary Adrenal Axis. The roles of projections to cortical circuits remain less well understood, but may be involved in regulating cortical arousal and the cognitive responses to stress and could represent promising targets for drug development to treat stress-related cognitive dysfunction. The aim of this project is to resolve the mechanisms by which orexinergic neurons directly modulate cortical network activity, using optogenetic stimulation of orexinergic projections in ex vivo cortical brain slices in combination with patch-clamp recordings, multiphoton imaging and high density multielectrode arrays.
Conscious perception in mammals depends on precise circuit connectivity between cerebral cortex and thalamus. During the wiring of reciprocal thalamus-cortex connections, thalamocortical axons (TCAs) first navigate forebrain regions that had undergone substantial evolutionary modifications. In mammals, transient cell populations in internal capsule and early corticofugal projections from subplate neurons closely interact with TCAs to guide pathfinding through ventral forebrain and pallial subpallial boundary (PSPB) crossing. Prior to TCA arrival, cortical areas are initially patterned by intrinsic genetic factors. TCAs then innervate cortex in a topographically organised manner to enable sensory input to refine cortical arealization. We investigate the mechanisms underlying the reciprocal influence between thalamus and cortex during development in rodent and in human. We recently demonstrated that these axons exhibited a close anatomical relationship with the existing germinal compartments in human. By 17 PCW, TCA did not only reach the transient subplate, a well-known target for thalamic axons in the mammalian brain, but also appeared to project toward the outer subventricular zone (OSVZ). We are using transcriptomic and proteomic approaches to explore the unique target compartments of the developing cortex, such as the OSVZ and suplate. We recently identified candidates that could mediate these interaction through paracrine mechanisms by secretion of neuroactive peptides.
Neural communication in the adult nervous system is mediated primarily through chemical synapses, where action potentials elicit Ca2+ signals, which trigger vesicular fusion and neurotransmitter release in the presynaptic compartment. At early stages of development, the brain is shaped by communication via trophic factors and other extracellular signalling, and by contact-mediated cell–cell interactions including chemical synapses. The patterns of early neuronal impulses and spontaneous and regulated neurotransmitter release guide the precise topography of axonal projections and contribute to determining cell survival. We study of the role of specific proteins of the synaptic vesicle release machinery in the establishment, plasticity, and maintenance of neuronal connections during development. We examine mouse models where various members of the N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex have been genetically manipulated (e.g. Snap25 or Munc13). We are focusing on the role of regulated vesicular release and/or cellular excitability in synaptic assembly, development and maintenance of cortical circuits, cell survival, circuit level excitation–inhibition balance, myelination, refinement, and plasticity of key axonal projections from the cerebral cortex. These models are important for understanding various developmental and psychiatric conditions, and neurodegenerative diseases.
Behaviour is not learned and driven by single brain regions, but instead arises from cooperation across multiple areas. One prominent circuit of interdependent regions consists of a loop between the cortex, basal ganglia, and thalamus. Together, these regions are critical for learning and executing behaviour, though it is largely unknown how this is accomplished at the level of neural activity. Our lab is interested in discovering fundamental principles of this circuit, and we investigate issues like how activity flows between regions, how it changes with learning, and how activity relates to behaviour. Our experiments combine large-scale imaging and electrophysiology techniques with learned behaviours and neuronal manipulation in mice. We use simple tasks, like stimulus-response associations, to investigate the relationship between activity and behaviour. Projects in the lab can be flexible along these themes, and may typically include recording and analysis from one or more brain regions across learning.
Heart Failure (HF) is a rapidly growing public health issue with an estimated prevalence of >37.7 million individuals globally and is a major unmet clinical need. HF is underpinned by cardiomyocyte hypertrophy, interstitial fibrosis, pathological remodelling and ultimately death. Current interventions do not prevent disease progression and cannot restore heart function. A critical contributor to chronic decline of cardiac function in HF is the immune system, notably the adaptive immune response. Following tissue damage there is release of cardiac antigens, such as α-myosin heavy chain (α-MHC), which are captured by dendritic cells (DCs) and presented to T-cells in the draining lymph nodes, inducing an auto-reactive T-cell response. This is due, in part, to T-cells escaping central tolerance towards cardiac self-antigens during development in the thymus. Activation of T-cells, primed against cardiac antigens, is seen as a possible mechanism for prolonged cardiac injury well after the initial insult. In support of this, anti-heart autoantibodies against cardiac epitopes are a well-known clinical epiphenomenon during HF and the presence of autoreactive T-cells post-MI has previously been demonstrated. This project will focus on understanding the mechanisms behind T-cells escaping central tolerance towards cardiac self-antigens during development in the thymus, and whether restoring this tolerance improves disease progression in HF.
A major obstacle to a deeper understanding of how the human heart responds to injury is the lack of human-derived in vitro 2D and 3D cell culture models that faithfully recapitulate the complexity of an in vivo system, where multiple resident and infiltrating cell populations co-exist and interact within the cardiac niche. Our group is working towards the development and application of self-organizing multi-lineage cardiac organoid structures to account for the complex 3D cell-cell interactions occurring between multiple cardiac cell types. We aim to facilitate translational research by enabling genetic screens and pharmacological modulation of disease states by further developing a human 3D vascularised cardiac organoid model that offers a chamber-specific, scalable and highly manipulable multi-lineage human cardiac model that reduces dependence on animal models.
Myocardial infarction (MI) causes permanent heart tissue loss in adult mammals. Following an MI, the injured heart recruits a significant number of monocyte-derived macrophages, essential immune cells that play critical roles in both scar formation and tissue regeneration. However, we still have limited understanding of the specific factors influencing distinct macrophage functions within the damaged heart. This project aims to shed light on how macrophage heterogeneity is linked to their spatial distribution across the heart and how, in turn, this distribution shapes macrophage identity and function. Despite their vital roles in cardiac repair, the intricate local environmental cues and cell-cell interactions governing the diverse roles of macrophages in this context have not been fully deciphered. By comprehending the regenerative microenvironment, where the innate immune response persists while still supporting regeneration, and by targeting macrophage-induced pro-fibrotic pathways, we may develop therapeutic strategies that harness pro-regenerative responses in the injured mammalian heart.
We investigate mechanisms of embryonic heart formation to inform novel strategies to promote regeneration of the adult mammalian heart, for example after myocardial infarction. We have a particular interest in stimulating new coronary vessel growth and in the role of the outer layer epicardium in promoting neovascularisation and regeneration. Following injury, there is a partial recapitulation of embryonic processes that drive coronary vessel growth, yet fundamental differences in the regulatory pathways limit the efficacy of the adult response. Comparative analyses allow us to identify key mechanisms that may be targeted in the adult mammalian heart to enhance repair. Our research in murine models is complemented with the use of human iPSC-derived models of coronary vascular development. Due to their fundamental role in heart development, epicardium-derived cells (EPDCs) have emerged as a tractable progenitor population with potential to regenerate myocardium and coronary vasculature. Mobilisation of EPDCs into the adult myocardium requires the identification of “embryonic” stimuli that promote epicardial activation and mesenchymal transformation. Ongoing research therefore investigates the mechanisms controlling the transition from active (embryonic) to quiescent (adult) state, as well as the signalling pathways through which the embryonic epicardium stimulates expansion of the coronary vasculature.
Congenital heart disease (CHD), where a baby’s heart does not form properly in the womb, is the most common birth defect, affecting 1% of all babies. Even with the advent of modern surgical correction techniques, it is the major cause of infant mortality and morbidity, requiring lifelong medical treatment. However, we do not always know why it happens. One-third of cases result from a genetic fault, but in the other two-thirds of cases the cause is less clear. Some of the latter result from the embryo being exposed to an abnormal environment in the womb in early pregnancy. This project will investigate the effects of one particular, highly prevalent environmental factor (maternal diabetes) on embryonic development using a mouse model system. Both type I and type II diabetes in humans can cause a suite of birth defects including severe CHD. However, little is known of how maternal diabetes effects embryonic heart development. We have created a mouse model that recapitulates the CHD seen in humans. This project will use a combination of morphological and molecular methods to discover how this factor causes CHD.
In this project, you will receive extensive training in cutting edge bioinformatic, single cell genomic, flow cytometry and in vivo gene expression analysis, techniques that are broadly used to address scientific questions across disciplines in academia and industry. Experiments will address two overarching aims that will build on our recent findings. AIM1: Molecular and functional characterization of distinct angioblast populations. We aim to perform a molecular characterisation of distinct angioblast populations and their derivatives using bioinformatic analyses of existing data, single cell multiome analyses of isolated ECs and their progenitors, and histological analyses using in situ hybridisation and immunofluorescence analyses throughout embryonic development. AIM 2: Genetic dissection of angioblast populations using a novel Etv2DreERT2 knock-in mouse model. To determine the functional importance of ECs derived from distinct sources, we will analyse a novel mouse model for intersectional genetics that will allow us to specifically target ECs derived from distinct angioblast populations.
“Novel insights into tumour acidosis and hypoxia from analyses of mutations, phenotypes and blood oxygen transport” DPAG Supervisor: Pawel Swietach
Chronic obstructive pulmonary disease (COPD) affects 400 million people worldwide and is a leading cause of death. Smoking remains the major risk factor for this condition. Unfortunately, there has been little improvement in outcomes for patients with COPD over the last two decades, in part because we currently lack the ability to diagnosis the condition early, before irreversible damage has occurred in the lungs. In Oxford we have over recent years developed a new technology for the non-invasive assessment of lung function, which is based upon quantification of heterogeneity (‘unevenness’) of gas exchange within the lung, rather than measurements of overall lung function. Across several patient groups, including those with asthma, COPD and cystic fibrosis, this is showing promise as a highly-sensitive marker of early lung disease. In this project, we will test the hypothesis that our measurements of lung heterogeneity, which are made during a period of relaxed breathing through a mouthpiece, are sensitive enough to identify early lung disease in smokers in whom conventional measures of lung function are normal. Our aim is to develop a test for early COPD, which will allow therapeutic intervention prior to the development of irreversible lung disease.
Iron availability has the potential to influence exercise capacity through its effects on red blood cell production, particularly at altitude where the erythropoietic drive is elevated. However, there is increasing evidence that iron levels per se may also influence cardiorespiratory function through direct effects on the pulmonary vasculature, cardiac function and cellular metabolism. This project would build upon previous research in Oxford and elsewhere to characterise the relationship between iron status and cardiorespiratory function during hypoxia, which has implications not only for athletic performance at altitude, but also for patients with chronic hypoxic lung disease. The project would be based around the study of integrative physiology in human volunteers, but we work in synergy with Prof Samira Lakhal-Littleton, whose laboratory has expertise in the use of preclinical models to dissect the mechanisms by which iron influences physiology at both a cellular and a systemic level.
The hypoxia-inducible factor (HIF) signalling pathway regulates the cellular response to hypoxia, but also appears to coordinate systemic responses to hypoxia, including the pulmonary vascular and ventilatory responses. In humans, the role of the HIF pathway in cardiorespiratory physiology has been characterised to date mainly by studying small groups of patients with genetic disorders, for example those with mutations in the HIF proteins themselves, or in the associated prolyl hydroxylase domain (PHD) oxygen sensing enzymes. Recently, a number of drugs have been developed that influence HIF signalling. Roxadustat, for example, is licensed for treatment of renal anaemia, and acts by upregulating the HIF pathway through PHD inhibition. However, the effects of this drug on systemic responses to hypoxia are not well understood. This project, funded in part by a Medical Research Council award to Dr Mary Slingo, will initially examine the effects of roxadustat on physiological responses to hypoxia in healthy volunteers, with a view to longer term studies in patients receiving this drug in the clinical setting.
Cardiac disease remains the leading cause of death in the developed world, and better understanding of heart physiology and disease is needed to advance our prevention and treatment strategies. Many cardiac diseases, such as heart failure, are progressive and involve a complex network of remodelling at the cellular, as well as organ level. Oscillations of calcium levels in the nucleus of cardiac muscle cells are known to control gene transcription and cell health, and their dysregulation is implicated in the development of several disease. However, the ways of how the cardiac cells control their nuclear calcium levels remain relatively poorly understood. In this project, the student will use advanced cell imaging techniques to provide critical insights into how nuclear calcium levels in cardiac muscle cells are controlled, integrating the data in state-of-the-art computational models to provide an integrated understanding of the system. Dysregulation of nuclear calcium handling in disease will be subsequently explored, aiming to identify therapeutical targets to prevent disease progression and pathological remodelling. The ratio of experimental and computational work will be tailored to the student, and training will be provided in either.
The role of abnormal cardiac substrate metabolism in the development of many cardiovascular diseases and the therapeutic potential of interventions targeting cardiac substrate metabolism are unclear. Magnetic Resonance Imaging and Spectroscopy (MRI/MRS) have long been used to monitor cardiac structure and function. However, the application of MRI/MRS for metabolic imaging has been limited by an intrinsically low sensitivity. Hyperpolarized Magnetic Resonance (hp-MR) is a new technique that yields greater than 10,000-fold signal increases in MR images and enables unprecedented real-time visualization of the biochemical mechanisms of abnormal metabolism. This allows measurement of instantaneous rates of substrate uptake and enzymatic transformation in vivo, providing a sensitive assessment of disease and a new means to monitor treatment response. This project will explore the application of hp-MR in the study of cardiovascular disease, enabling the assessment of pyruvate metabolism through the key metabolic enzyme, pyruvate dehydrogenase, and how it can be modulated as a therapeutic target.
Hibernation is a widespread evolutionary strategy employed by many animal species to deal with adverse environmental conditions, such as food scarcity, low or high temperatures and climatic natural disasters. Hypometabolism is typically considered as an energy saving strategy, but it is employed acutely, for example in response to imminent threat, such as predation risk. Much research has been directed towards investigating peripheral bodily physiology during hibernation, but, surprisingly, the brain mechanisms of torpor, as well as the effects of hibernation on the brain remain under-investigated. Limited knowledge suggests that torpor represents a remarkable example of brain plasticity, reflected in massive synaptic remodelling upon entrance into and emergence from hibernation. Harnessing this capacity for human applications remains in its infancy. The proposed work will develop a novel approach, based on closed loop neuromodulation, which will enable a physiological induction of torpor, to investigate its effects on brain function, and to test the hypothesis that resetting brain networks through cycles of hibernation increases resilience to adverse conditions, including mental health conditions, such as PTSD and depression. In this project we aim to unravel physiological mechanisms involved in spontaneous entering of the state of hibernation in natural torpidators Phodopus sungorus. We will use a closed-loop approach where combined monitoring of brain activity and physiological parameters, such as levels of metabolism, body temperature and heart rate, will be dynamically coupled with relevant environmental factors, such as lighting, temperature and gaseous composition of air, to facilitate state transitions through stimulation of the brain and the autonomic nervous system in a physiologically relevant context. The key innovative element of this proposal is the new approach to harness hibernation-associated brain plasticity for treatment of mental health disorders, such as PTSD and depression. We will study how spontaneous and induced hypometabolism resets brain networks through synaptic remodelling, and investigate the role of sleep in homeostatic regulation of torpor-related synaptic plasticity.
Population ageing brings significant challenges to society and the economy. Sleep and cognitive problems are among the major complaints of the elderly, and insufficient or disrupted sleep has been linked to a broad range of neurological and neurodegenerative disorders. One of the most notable examples is Alzheimer’s disease, which has been directly linked with sleep disruption, and has no cure. It has been proposed that improving or enhancing sleep could have far-reaching health benefits beyond the improvement of sleep per se. Age-related changes in cognitive functions encompass a reduced capacity to learn new facts and skills (plasticity), as well as attentional and memory problems. It is well established that cortical synapses and firing rates are dynamically modulated by intrinsic, naturally occurring processes, of which sleep is of key significance. For instance, evidence suggests that during sleep some synaptic connections are strengthened, while others are weakened or eliminated, to allow bringing the overall synaptic strength to its homeostatic set point. Sleep also plays an important role in memory consolidation. According to the prevailing view, sleep and associated large-scale network oscillations, such as slow waves and sleep spindles, are necessary for the transfer of temporary memory traces from the hippocampus for long-term storage in the cortex, where they are integrated into existing memory schemata. Sleep disruption prevents consolidation of recent memories, and equally importantly, severely reduces the capacity for further learning. There is a great deal of interest in developing new approaches to improve sleep quality or enhance brain oscillations during sleep, and the possibility of non-invasive modulation of sleep oscillations has recently attracted significant attention. However, research in this areas is still rudimentary, and studies often yield contradictory results. It is well established that both sleep and psychedelic drugs exert a profound effect on neural activity across the brain, including changes to neuronal firing rates and the strength of synaptic connections. Our recent data suggest that in laboratory mice 5-MeO DMT and psilocin induce an altered state of vigilance, characterised by an intrusion of slow-wave activity – the key hallmark of NREM sleep – in the awake state. This finding is highly relevant given the established functional role of sleep in general, and slow-wave activity in particular in a broad range of restorative processes – from synaptic renormalisation to clearance of toxic by-products of metabolism. Not surprisingly, there are many studies currently underway aiming to artificially enhance sleep slow waves for therapeutic benefit. However, to the best of our knowledge, the possibility of using psychedelics as a tool to promote restorative processes in the brain in the context of ageing, and its associated risk for cognitive decline and neurodegeneration, has not been explored. We propose that enhancement of slow waves by psychedelics can restore the capacity for synaptic plasticity, which is especially relevant in the context of the ageing brain. My laboratory has a unique combination of relevant expertise – from fundamental sleep neurobiology, including sleep in ageing, to synaptic plasticity, psychedelics and closed-loop modulation of brain activity during sleep. We benefit from a highly stimulating interdisciplinary environment at DPAG, SCNi and KIND, and a long-term collaboration with Beckley Psytech Ltd. The proposed research has a strong potential to provide essential knowledge which will be used to develop innovative therapies for restoring the potential for synaptic plasticity in the ageing brain.
We seek highly motivated DPhil students with either a scientific or medical background to join our laboratory to work on the molecular mechanisms of neurological and neurodegenerative diseases. Techniques in molecular genetics have allowed the identification of genes and proteins with an important function in both familial and sporadic forms of Parkinson’s disease and Alzheimer’s disease. Our laboratory focusses on following up these genes and proteins to better understand disease mechanisms to identify potential therapeutic targets for further translational studies. To undertake this, we work with induced pluripotent stem cells (iPSCs) generated from patients with Parkinson’s, Alzheimer’s and related disorders. iPSC-derived patient models promise to revolutionize the study of neurodegenerative diseases in which the critical cell type has been previously inaccessible. The capability to generate, engineer, differentiate and phenotype iPSC-derived neurons and glia from patients with neurodegeneration allows for the study of highly physiological human models of disease. We have undertaken a detailed phenotypic analysis of patient and control iPSC-derived neurons and glia and identified and published strong cellular phenotypes using robust assays suitable for studying disease mechanisms across a range of new projects.
Exosomes are nano-sized vesicles secreted from the endosomal compartments of cells. They carry a multitude of different bioactive cargos, including proteins, RNAs and lipids that can reprogramme target cells. Exosomes have been implicated in many pathologies, in particular cancer, where they can prime pre-metastatic sites, induce drug resistance and suppress the immune system. However, they are also involved in complex physiological cell-cell signalling events. For example, we found that exosomes produced in the male accessory gland of the fruit fly reprogramme female behaviour, so she rejects other males that try to mate with her. Using this fly model in which exosomes are made inside unusually large intracellular compartments that can be imaged in real-time, we identified a novel evolutionarily conserved exosome subtype, called Rab11-exosomes, which is the primary mediator of key physiological and cancer-relevant exosome functions, despite representing a small fraction of all secreted vesicles. We recently identified multiple new conserved regulators of Rab11-exosomes by combining human Rab11-exosome proteomics with fly genetic analysis. This project will involve analysing these regulators further, focusing on how they shape Rab11-exosomes, coat them with extravesicular proteins and traffic them to the cell surface, mechanisms that are all potential targets for future exosome subtype-specific therapies.
Cell-cell communication controls almost all physiological processes in multicellular organisms and is defective in many diseases. Our group has developed the male reproductive accessory gland in the fruit fly Drosophila melanogaster as a new genetic model to study the fundamental processes in secretion and signalling. Employing this system, we discovered that multiple secreted signals, including Sex Peptide, the central regulator of female post-mating responses, are packaged into lipophilic structures that we call microcarriers, which stabilise these proteins in the gland and then permit their rapid release when deposited in the female uterus. We have now found that evolutionarily conserved derivatives of the lipid ceramide and the enzymes that produce them have multiple roles in generating microcarriers. In humans, components of this microcarrier biogenesis pathway are required for several biological processes in humans, are highly upregulated in cancer and implicated in metabolic disease and obesity. In this project, additional new evolutionarily conserved regulators of microcarriers that we have recently identified will be characterised using advanced genetic and imaging technologies to determine their functions. We anticipate that this work could provide the stepping stone to extend our studies into human cells and assess the relevance of microcarriers to human health and disease.
Amyloidogenesis, the aggregation of soluble proteins into insoluble fibrils, has multiple biological functions in health and disease, eg, in Alzheimer’s Disease (AD), aggregations of A-beta peptides, cleaved products of Amyloid Precursor Protein (APP), form plaques, while peptide hormones naturally condense into insoluble, dense-core granules (DCGs), stored within secretory vesicles until release. However, in vivo assays to analyse how amyloidogenesis is initiated are lacking. We have developed a new cellular model for DCG biogenesis, the Drosophila prostate-like secondary cell (SC). These cells have highly enlarged (5 micron diameter) DCG compartments, permitting the rapid process of DCG assembly to be followed by light and fluorescence microscopy in real-time. We find DCG formation requires the fly homologues of APP, called APPL, and another amyloidogenic protein, TGF-beta-induced, as well as intraluminal vesicles that are secreted as so-called Rab11-exosomes. Genetic dissection of the DCG biogenesis process in SCs shows that it is disrupted by mutant proteins linked to AD, producing several AD-like phenotypes, and strongly suggests that these previously unsuspected defects are key triggers in pathology. This project will characterise this process further in flies and investigate how pathological defects can be suppressed by genetic manipulations, drugs and dietary changes.
cAMP and its effector PKA are key regulators of cardiac function and defective cAMP/PKA signalling is a hallmark of heart failure (HF) and genetic cardiomyopathies. This signalling pathway is also at the core of current therapies, which however remain unsatisfactory and need improvement. Current therapeutic strategies largely ignore signalling processes occurring in cardiomyocytes at the subcellular level. We use FRET-based imaging approaches to measure cAMP/PKA signalling in real-time and with high spatio-temporal resolution. Using this approach we were able to directly show that cAMP/PKA signalling is highly compartmentalised within subcellular nanodomains (1, 2), with different sites affecting different functions (2). In a recent study we found that adrenergic stimulation generates pools of cAMP with different amplitude and kinetics at the plasmalemma and at the myofilaments and that such local regulation is disrupted in HF (2). Local PKA activity is dictated by local [cAMP], controlled at each specific site by particular adenylyl cyclases (AC) and phosphodiesterases (PDE) isoforms. Local phosphorylation of targets results from the balance of local PKA and phosphatase (PP) activity. All these components can potentially be manipulated to affect local signalling. Compartmentalization of signalling provides a unique opportunity to intervene therapeutically with increased precision by selectively targeting individual nanodomains to affect only the desired function. Recently, we have conducted an integrated PDE phospho-interactome ananlysis that unveiled multiple novel and non-obvious cAMP nanodomain under specific regulation of PDE isoforms (4). We are currently validating these data and characterising the function reglated by these novel nanodomans.The overall aim of our work is to build a detailed map of cAMP nanodomains in cardiac myocytes . The map will be used as a blueprint to assess alterations in pathological conditions to gain novel mechanistic understanding of pathological processes at the molecular level. This information will guide development of new strategies for targeted therapeutic interventions.The project will test novel FRET-based reporters targeted to specific subcellular sites in cardiac myocytes to establish local cAMP dynamics at key signalling nodes that participate in the regulation of cardiac myocyte function. The work will involve biochemical and genetic approaches to study cAMP signalling at these sites in animal models of HF and in human cardiac myocytes differentiated from inducible pluripotent stem cells.
The brain microenvironment is tightly regulated by the blood–brain barrier (BBB) which maintains the central nervous system internal milieu. BBB leakage following neuroinflammation (or systemic inflammation) has recently been described early in the occurrence and development of neurodegenerative disorders including Parkinson’s, Alzheimer's, and cerebral small vessel disease. Dynamic 3D models of the BBB represent a major advance on traditional static 2D models allowing cells to be in a physiologically realistic native-like 3D environment that faithfully recapitulate the complexity of an in vivo system without artificial support membranes. We seek highly motivated DPhil students with either a scientific or medical background to join our group to work on the molecular mechanisms of BBB (dys)function in neurodegeneration. In this project, you will combine the use of patient-derived induced pluripotent stem cells (iPSCs) together with novel brain-on-a-chip platforms, advanced microscopy, microfluidics, and molecular assays. This project will advance our ability to understand how does inflammation-mediated BBB dysfunction lead to the development of neurodegeneration and dementia. It will establish a framework to address fundamental questions about the role of the BBB in health and neurodegeneration.
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